TRON: The Ghost in the Machine was the first true comic to feature the TRON Universe and continues the story of Jet Bradley, the protagonist of TRON 2.0. The six-issue mini-series comic debuted on April 26th, 2006 and the last issue was released on September 10th, 2008.

In 2003, a comic entitled, TRON 2.0: Derezzed was announced by comic book publisher 88 MPH. However, that comic was canceled before any issues were released. In 2005, Slave Labor Graphics Publishing (aka SLG) announced that they were doing a six-issue comic that would continue the storyline of TRON 2.0. Along with TRON: The Ghost in the Machine, SLG also published three other comics based on Disney licenses: Haunted Mansion, Alice in Wonderland, and Gargoyles.

The story revolves around a program that believes itself to be a user named Jet Bradley, son of the original Tron programmer Alan Bradley. This version of Jet is a backup copy of the real Jet Bradley, who explored the digital universe in TRON 2.0. He has been split into three distinct aspects, represented by color (red, blue and green), all at war with each other. Eventually the fractured program of Jet converges into one being, resulting in a white "User" version. The program then comes face to face with his user and is given a chance, using the Tron Legacy Code integrated into his identity disc as a key, to be transferred into the real world. The unified Jet declines, as his presence is the only thing keeping the digital universe he exists within stable and his exiting would mean the deresolution of everyone he knows within the computer. He releases the Tron Legacy Code from his disc and restores the digital world, accepting his life as a computer program.

The comic was written Landry Walker and Eric Jones, who have both previously worked on other SLG comics such as Little Gloomy, Kid Gravity. Walker is a member of the Tron-Sector forums under the username "lurkinghorror".

The artwork of the first two issues were drawn by Louie De Martinis, a relative newcomer to comic books, who was originally an animator. The remainder of the issues were drawn by Mike Shoyket.

The comic is the first official TRON media to mention Tron-Sector in their credits.